Version checked for this guide: 1.0.11 · 2026-09-23
Start with converted mzML/mzXML files in a dedicated processing directory, normally grouped into sample-type subdirectories such as QC and Subject. Run positive and negative modes separately. process_data() performs raw-data processing and writes outputs under Result.
Set ppm from instrument performance, peakwidth in seconds from chromatography, and signal/noise, prefilter and noise using representative files. bw and min_fraction affect across-sample grouping. fill_peaks controls chromatographic gap filling, not statistical imputation. Reduce threads when memory is limiting.
Review TIC/BPC, RT correction, the peak table and extracted EICs. Preserve intermediate files if later inspection requires them. The parameter values below are an example, not a validated method for your instrument. Inspect output files after the call; do not assume its return value is the final dataset.
Functional scope
Raw processing; EIC extraction; chromatogram visualization; adjusted-RT visualization; targeted-table validation.
Example
# Requires your converted files under analysis/MS1/.
# massprocesser::process_data(
# path = "analysis/MS1", polarity = "positive",
# ppm = 15, peakwidth = c(5, 30), snthresh = 10,
# threads = 2, min_fraction = 0.5, fill_peaks = FALSE,
# output_tic = TRUE, output_bpc = TRUE
# )
help("process_data", package = "massprocesser")
Find a function
The checked source exports the following APIs, including compatibility interfaces and utilities. Consult the installed version with help("function_name", package = "massprocesser") for argument details.
Show exported functions
check_targeted_table, extract_eic, get_massprocesser_version, massprocesser_conflicts, massprocesser_logo, massprocesser_packages, plot_adjusted_rt, plot_chromatogram, process_data
Package source and reference documentation · Complete workflow